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Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing.
Lhomme, Sébastien; Latour, Justine; Jeanne, Nicolas; Trémeaux, Pauline; Ranger, Noémie; Migueres, Marion; Salin, Gérald; Donnadieu, Cécile; Izopet, Jacques.
  • Lhomme S; Infinity, Université Toulouse, CNRS, INSERM, UPS, 31300 Toulouse, France.
  • Latour J; Laboratoire de Virologie, CHU Toulouse, Hôpital Purpan, 31300 Toulouse, France.
  • Jeanne N; Laboratoire de Virologie, CHU Toulouse, Hôpital Purpan, 31300 Toulouse, France.
  • Trémeaux P; Laboratoire de Virologie, CHU Toulouse, Hôpital Purpan, 31300 Toulouse, France.
  • Ranger N; Laboratoire de Virologie, CHU Toulouse, Hôpital Purpan, 31300 Toulouse, France.
  • Migueres M; Laboratoire de Virologie, CHU Toulouse, Hôpital Purpan, 31300 Toulouse, France.
  • Salin G; Infinity, Université Toulouse, CNRS, INSERM, UPS, 31300 Toulouse, France.
  • Donnadieu C; Laboratoire de Virologie, CHU Toulouse, Hôpital Purpan, 31300 Toulouse, France.
  • Izopet J; INRAE, US 1426, GeT-PlaGe, Genotoul, 31326 Castanet-Tolosan, France.
Viruses ; 13(12)2021 12 18.
Article in English | MEDLINE | ID: covidwho-1580423
ABSTRACT
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is the causal agent of the COVID-19 pandemic that emerged in late 2019. The outbreak of variants with mutations in the region encoding the spike protein S1 sub-unit that can make them more resistant to neutralizing or monoclonal antibodies is the main point of the current monitoring. This study examines the feasibility of predicting the variant lineage and monitoring the appearance of reported mutations by sequencing only the region encoding the S1 domain by Pacific Bioscience Single Molecule Real-Time sequencing (PacBio SMRT). Using the PacBio SMRT system, we successfully sequenced 186 of the 200 samples previously sequenced with the Illumina COVIDSeq (whole genome) system. PacBio SMRT detected mutations in the S1 domain that were missed by the COVIDseq system in 27/186 samples (14.5%), due to amplification failure. These missing positions included mutations that are decisive for lineage assignation, such as G142D (n = 11), N501Y (n = 6), or E484K (n = 2). The lineage of 172/186 (92.5%) samples was accurately determined by analyzing the region encoding the S1 domain with a pipeline that uses key positions in S1. Thus, the PacBio SMRT protocol is appropriate for determining virus lineages and detecting key mutations.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Sequence Analysis, DNA / Spike Glycoprotein, Coronavirus / SARS-CoV-2 Type of study: Prognostic study Topics: Variants Limits: Humans Language: English Year: 2021 Document Type: Article Affiliation country: V13122544

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Sequence Analysis, DNA / Spike Glycoprotein, Coronavirus / SARS-CoV-2 Type of study: Prognostic study Topics: Variants Limits: Humans Language: English Year: 2021 Document Type: Article Affiliation country: V13122544